Speed setting, mouse stage/beam control, and remote cameras

src/instamatic/gui/autocred_frame.py

@@ -13,10 +13,10 @@
 from instamatic.calibrate import CalibBeamShift
 from instamatic.calibrate.filenames import *
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 
-class ExperimentalautocRED(LabelFrame, HasQMixin):
+class ExperimentalautocRED(LabelFrame, ModuleFrameMixin):
     """Data collection protocol for SerialRED data collection on a high-speed
     Timepix camera using automated screening and crystal tracking.
 

src/instamatic/gui/base_module.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from queue import Queue
+from typing import Any
 
 
 class BaseModule:
@@ -35,7 +36,8 @@ def initialize(self, parent):
         return frame
 
 
-class HasQMixin:
-    """Asserts module.q remains reserved for DataCollectionController.q."""
+class ModuleFrameMixin:
+    """Asserts some class attributes i.e. module.q, app remain reserved."""
 
     q: Queue
+    app: Any

src/instamatic/gui/click_dispatcher.py

@@ -82,9 +82,11 @@ def add_listener(
         self,
         name: str,
         callback: Optional[Callable[[ClickEvent], None]] = None,
+        active: bool = False,
     ) -> ClickListener:
         """Convenience method that adds and returns a new `ClickListener`"""
         listener = ClickListener(name, callback)
+        listener.active = active
         self.listeners[name] = listener
         return listener
 

src/instamatic/gui/cred_fei_frame.py

@@ -5,10 +5,10 @@
 
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 
-class ExperimentalcRED_FEI(LabelFrame, HasQMixin):
+class ExperimentalcRED_FEI(LabelFrame, ModuleFrameMixin):
     """Simple panel to assist cRED data collection (mainly rotation control) on
     a FEI microscope."""
 

src/instamatic/gui/cred_frame.py

@@ -6,12 +6,12 @@
 
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
-ENABLE_FOOTFREE_OPTION = False
+ENABLE_FOOTFREE_OPTION = True
 
 
-class ExperimentalcRED(LabelFrame, HasQMixin):
+class ExperimentalcRED(LabelFrame, ModuleFrameMixin):
     """GUI panel for doing cRED experiments on a Timepix camera."""
 
     def __init__(self, parent):

src/instamatic/gui/cred_tvips_frame.py

@@ -9,12 +9,12 @@
 from instamatic import config
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 barrier = threading.Barrier(2, timeout=60)
 
 
-class ExperimentalTVIPS(LabelFrame, HasQMixin):
+class ExperimentalTVIPS(LabelFrame, ModuleFrameMixin):
     """GUI panel for doing cRED / SerialRED experiments on a TVIPS camera."""
 
     def __init__(self, parent):

src/instamatic/gui/ctrl_frame.py

@@ -2,18 +2,22 @@
 
 import queue
 import threading
-from threading import Event
 from tkinter import *
 from tkinter.ttk import *
-from typing import Dict
+
+import numpy as np
 
 from instamatic import config
+from instamatic.calibrate import CalibBeamShift
+from instamatic.calibrate.filenames import CALIB_BEAMSHIFT
+from instamatic.exceptions import TEMCommunicationError
+from instamatic.gui.click_dispatcher import ClickEvent, MouseButton
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 
-class ExperimentalCtrl(LabelFrame, HasQMixin):
+class ExperimentalCtrl(LabelFrame, ModuleFrameMixin):
     """This panel holds some frequently used functions to control the electron
     microscope."""
 
@@ -74,21 +78,31 @@ def __init__(self, parent):
         )
         b_wobble.grid(row=4, column=2, sticky='W', columnspan=2)
 
+        text = 'Move stage with LMB'
+        self.lmb_stage = Checkbutton(frame, text=text, variable=self.var_lmb_stage)
+        self.lmb_stage.grid(row=1, column=3, columnspan=3, sticky='W')
+        self.var_lmb_stage.trace_add('write', self.toggle_lmb_stage)
+
+        text = 'Move beam with RMB'
+        self.rmb_beam = Checkbutton(frame, text=text, variable=self.var_rmb_beam)
+        self.rmb_beam.grid(row=2, column=3, columnspan=3, sticky='W')
+        self.var_rmb_beam.trace_add('write', self.toggle_rmb_beam)
+
         e_stage_x = Spinbox(frame, textvariable=self.var_stage_x, **stage)
         e_stage_x.grid(row=6, column=1, sticky='EW')
         e_stage_y = Spinbox(frame, textvariable=self.var_stage_y, **stage)
         e_stage_y.grid(row=6, column=2, sticky='EW')
         e_stage_z = Spinbox(frame, textvariable=self.var_stage_z, **stage)
         e_stage_z.grid(row=6, column=3, sticky='EW')
 
+        Label(frame, text='Rotation speed', width=20).grid(row=5, column=0, sticky='W')
+        e_goniotool_tx = Spinbox(
+            frame, width=10, textvariable=self.var_goniotool_tx, from_=1, to=12, increment=1
+        )
+        e_goniotool_tx.grid(row=5, column=1, sticky='EW')
+        b_goniotool_set = Button(frame, text='Set', command=self.set_goniotool_tx)
+        b_goniotool_set.grid(row=5, column=2, sticky='EW')
         if config.settings.use_goniotool:
-            Label(frame, text='Rot. Speed', width=20).grid(row=5, column=0, sticky='W')
-            e_goniotool_tx = Spinbox(
-                frame, width=10, textvariable=self.var_goniotool_tx, from_=1, to=12, increment=1
-            )
-            e_goniotool_tx.grid(row=5, column=1, sticky='EW')
-            b_goniotool_set = Button(frame, text='Set', command=self.set_goniotool_tx)
-            b_goniotool_set.grid(row=5, column=2, sticky='W')
             b_goniotool_default = Button(
                 frame, text='Default', command=self.set_goniotool_tx_default
             )
@@ -212,6 +226,8 @@ def init_vars(self):
         self.var_diff_defocus_on = BooleanVar(value=False)
 
         self.var_stage_wait = BooleanVar(value=True)
+        self.var_lmb_stage = BooleanVar(value=False)
+        self.var_rmb_beam = BooleanVar(value=False)
 
     def set_mode(self, event=None):
         self.ctrl.mode.set(self.var_mode.get())
@@ -257,7 +273,12 @@ def set_positive_angle(self):
     def set_goniotool_tx(self, event=None, value=None):
         if not value:
             value = self.var_goniotool_tx.get()
-        self.ctrl.stage.set_rotation_speed(value)
+        try:
+            self.ctrl.stage.set_rotation_speed(value)
+        except AttributeError:
+            print('This TEM does not implement `setRotationSpeed` method')
+        except TEMCommunicationError:
+            print('Could not connect to the stage rotation speed controller')
 
     def set_goniotool_tx_default(self, event=None):
         value = 12
@@ -301,6 +322,54 @@ def toggle_alpha_wobbler(self):
             if self.wobble_stop_event:
                 self.wobble_stop_event.set()
 
+    def toggle_lmb_stage(self, _name, _index, _mode):
+        """If self.var_lmb_stage, move stage using Left Mouse Button."""
+
+        d = self.app.get_module('stream').click_dispatcher
+        if self.var_lmb_stage.get():
+            try:
+                stage_matrix = self.ctrl.get_stagematrix()
+            except KeyError:
+                print('No stage matrix for current mode and magnification found.')
+                print('Run `instamatic.calibrate_stagematrix` to use this feature.')
+                self.var_lmb_stage.set(False)
+                return
+
+            def _callback(click: ClickEvent) -> None:
+                if click.button == MouseButton.LEFT:
+                    cam_dim_x, cam_dim_y = self.ctrl.cam.get_camera_dimensions()
+                    pixel_delta = np.array([click.y - cam_dim_y / 2, click.x - cam_dim_x / 2])
+                    stage_shift = np.dot(pixel_delta, stage_matrix)
+                    x, y = self.ctrl.stage.xy
+                    self.ctrl.stage.set(x=x + stage_shift[0], y=y + stage_shift[1])
+
+            d.add_listener('lmb_stage', _callback, active=True)
+        else:
+            d.listeners.pop('lmb_stage', None)
+
+    def toggle_rmb_beam(self, _name, _index, _mode) -> None:
+        """If self.var_rmb_beam, move beam using Right Mouse Button."""
+
+        d = self.app.get_module('stream').click_dispatcher
+        if self.var_rmb_beam.get():
+            path = self.app.get_module('io').get_experiment_directory().parent / 'calib'
+            try:
+                calib_beamshift = CalibBeamShift.from_file(path / CALIB_BEAMSHIFT)
+            except OSError:
+                print(f'No {CALIB_BEAMSHIFT} file in directory {path} found.')
+                print('Run `instamatic.calibrate_beamshift` there to use this feature.')
+                self.var_rmb_beam.set(False)
+                return
+
+            def _callback(click: ClickEvent) -> None:
+                if click.button == MouseButton.RIGHT:
+                    bs = calib_beamshift.pixelcoord_to_beamshift((click.y, click.x))
+                    self.ctrl.beamshift.set(*[float(b) for b in bs])
+
+            d.add_listener('rmb_beam', _callback, active=True)
+        else:
+            d.listeners.pop('rmb_beam', None)
+
     def stage_stop(self):
         self.q.put(('ctrl', {'task': 'stage.stop'}))
 

src/instamatic/gui/debug_frame.py

@@ -8,7 +8,7 @@
 
 from instamatic import config
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 scripts_drc = config.locations['scripts']
 
@@ -22,7 +22,7 @@
 VMPORT = config.settings.VM_server_port
 
 
-class DebugFrame(LabelFrame, HasQMixin):
+class DebugFrame(LabelFrame, ModuleFrameMixin):
     """GUI panel with advanced / debugging functions."""
 
     def __init__(self, parent):

src/instamatic/gui/fast_adt_frame.py

@@ -8,7 +8,7 @@
 from instamatic import controller
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 pad0 = {'sticky': 'EW', 'padx': 0, 'pady': 1}
 pad10 = {'sticky': 'EW', 'padx': 10, 'pady': 1}
@@ -82,7 +82,7 @@ def as_dict(self):
         return {n: v.get() for n, v in vars(self).items() if isinstance(v, Variable)}
 
 
-class ExperimentalFastADT(LabelFrame, HasQMixin):
+class ExperimentalFastADT(LabelFrame, ModuleFrameMixin):
     """GUI panel to perform selected FastADT-style (c)RED & PED experiments."""
 
     def __init__(self, parent):

src/instamatic/gui/gui.py

@@ -43,6 +43,8 @@ def __init__(self, ctrl=None, stream=None, beam_ctrl=None, app=None, log=None):
         for module in self.app.modules.values():
             if 'q' in get_type_hints(module.__class__):
                 module.q = getattr(module, 'q', self.q)
+            if 'app' in get_type_hints(module.__class__):
+                module.app = getattr(module, 'app', self.app)
 
         self.exitEvent = threading.Event()
         atexit.register(self.exitEvent.set)
@@ -136,11 +138,11 @@ def __init__(self, root, cam, modules: list = []):
         self.app = AppLoader()
 
         # the stream window is a special case, because it needs access
-        # to the cam module and the AppLoader itself
+        # to the cam module
         if cam:
             from .videostream_frame import module as stream_module
 
-            stream_module.set_kwargs(stream=cam, app=self.app)
+            stream_module.set_kwargs(stream=cam)
             modules.insert(0, stream_module)
 
         self.module_frame = Frame(root)

src/instamatic/gui/machine_learning_frame.py

@@ -10,7 +10,7 @@
 
 from instamatic.formats import read_image
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 from .mpl_frame import ShowMatplotlibFig
 
 
@@ -25,7 +25,7 @@ def treeview_sort_column(tv, col, reverse):
     tv.heading(col, command=lambda: treeview_sort_column(tv, col, not reverse))
 
 
-class MachineLearningFrame(LabelFrame, HasQMixin):
+class MachineLearningFrame(LabelFrame, ModuleFrameMixin):
     """GUI Panel to read in the results from the machine learning algorithm to
     identify good/poor crystals based on their diffraction pattern."""
 

src/instamatic/gui/red_frame.py

@@ -5,10 +5,10 @@
 
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 
-class ExperimentalRED(LabelFrame, HasQMixin):
+class ExperimentalRED(LabelFrame, ModuleFrameMixin):
     """GUI panel to perform a simple RED experiment using discrete rotation
     steps."""
 

src/instamatic/gui/sed_frame.py

@@ -9,7 +9,7 @@
 from instamatic.calibrate import CalibDirectBeam
 from instamatic.calibrate.filenames import CALIB_BEAMSHIFT, CALIB_DIRECTBEAM
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 # import matplotlib
 # matplotlib.use('TkAgg')
@@ -50,7 +50,7 @@
 Press <OK> to start"""
 
 
-class ExperimentalSED(LabelFrame, HasQMixin):
+class ExperimentalSED(LabelFrame, ModuleFrameMixin):
     """GUI panel to start a SerialED experiment."""
 
     def __init__(self, parent):

src/instamatic/gui/videostream_frame.py

@@ -15,24 +15,23 @@
 
 from instamatic._typing import AnyPath
 from instamatic.formats import read_tiff, write_tiff
-from instamatic.gui.base_module import BaseModule, HasQMixin
+from instamatic.gui.base_module import BaseModule, ModuleFrameMixin
 from instamatic.gui.click_dispatcher import ClickDispatcher
 from instamatic.gui.videostream_processor import VideoStreamProcessor
 from instamatic.processing import apply_flatfield_correction
 from instamatic.utils.spinbox import Spinbox
 
 
-class VideoStreamFrame(LabelFrame, HasQMixin):
+class VideoStreamFrame(LabelFrame, ModuleFrameMixin):
     """GUI panel to continuously display the last frame streamed from the
     camera."""
 
-    def __init__(self, parent, stream, app=None):
+    def __init__(self, parent, stream):
         LabelFrame.__init__(self, parent, text='Stream')
 
         self.parent = parent
 
         self.stream = stream
-        self.app = app
 
         self.panel = None